Starting phenix.real_space_refine on Sun Oct 12 17:21:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tgu_41244/10_2025/8tgu_41244.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tgu_41244/10_2025/8tgu_41244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tgu_41244/10_2025/8tgu_41244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tgu_41244/10_2025/8tgu_41244.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tgu_41244/10_2025/8tgu_41244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tgu_41244/10_2025/8tgu_41244.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 13539 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 9258 2.51 5 N 2475 2.21 5 O 3039 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14880 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4518 Classifications: {'peptide': 573} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 549} Chain breaks: 4 Chain: "B" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4518 Classifications: {'peptide': 573} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 549} Chain breaks: 4 Chain: "C" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4518 Classifications: {'peptide': 573} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 548} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 3.53, per 1000 atoms: 0.24 Number of scatterers: 14880 At special positions: 0 Unit cell: (132.84, 129.6, 129.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 3039 8.00 N 2475 7.00 C 9258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.04 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.04 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 605 " distance=2.05 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.04 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " BMA S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A 701 " - " ASN A 618 " " NAG A 705 " - " ASN A 234 " " NAG A 706 " - " ASN A 339 " " NAG A 707 " - " ASN A 355 " " NAG A 708 " - " ASN A 386 " " NAG B 701 " - " ASN B 611 " " NAG B 704 " - " ASN B 262 " " NAG B 706 " - " ASN B 301 " " NAG B 707 " - " ASN B 355 " " NAG B 708 " - " ASN B 363 " " NAG C 704 " - " ASN C 133 " " NAG C 705 " - " ASN C 185 " " NAG C 706 " - " ASN C 339 " " NAG C 707 " - " ASN C 355 " " NAG C 708 " - " ASN C 363 " " NAG C 709 " - " ASN C 392 " " NAG D 1 " - " ASN A 88 " " NAG E 1 " - " ASN A 160 " " NAG F 1 " - " ASN A 197 " " NAG G 1 " - " ASN A 262 " " NAG H 1 " - " ASN A 276 " " NAG I 1 " - " ASN A 295 " " NAG J 1 " - " ASN A 301 " " NAG K 1 " - " ASN A 332 " " NAG L 1 " - " ASN A 363 " " NAG M 1 " - " ASN A 392 " " NAG N 1 " - " ASN A 448 " " NAG O 1 " - " ASN B 156 " " NAG P 1 " - " ASN B 160 " " NAG Q 1 " - " ASN B 197 " " NAG R 1 " - " ASN B 234 " " NAG T 1 " - " ASN B 276 " " NAG V 1 " - " ASN B 332 " " NAG W 1 " - " ASN B 339 " " NAG X 1 " - " ASN B 392 " " NAG Y 1 " - " ASN B 448 " " NAG a 1 " - " ASN C 160 " " NAG b 1 " - " ASN C 197 " " NAG c 1 " - " ASN C 234 " " NAG e 1 " - " ASN C 276 " " NAG f 1 " - " ASN C 295 " " NAG g 1 " - " ASN C 301 " " NAG h 1 " - " ASN C 332 " " NAG i 1 " - " ASN C 386 " " NAG j 1 " - " ASN C 448 " Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 524.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 31 sheets defined 25.1% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.518A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.916A pdb=" N LYS A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.547A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.701A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 543 removed outlier: 4.036A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 596 removed outlier: 4.082A pdb=" N TRP A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 615 removed outlier: 3.530A pdb=" N SER A 615 " --> pdb=" O SER A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.584A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 650 removed outlier: 3.889A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 662 Processing helix chain 'B' and resid 99 through 117 Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.704A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 350 removed outlier: 3.735A pdb=" N LYS B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 475 through 481 removed outlier: 3.625A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 removed outlier: 4.098A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.287A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.544A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.796A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'B' and resid 650 through 662 Processing helix chain 'C' and resid 57 through 63 removed outlier: 4.224A pdb=" N TYR C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.308A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 334 through 354 removed outlier: 4.225A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.638A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 544 removed outlier: 4.242A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 544 " --> pdb=" O GLN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 596 removed outlier: 4.418A pdb=" N GLN C 575 " --> pdb=" O TRP C 571 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TRP C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 624 Processing helix chain 'C' and resid 627 through 633 Processing helix chain 'C' and resid 638 through 649 Processing helix chain 'C' and resid 650 through 663 removed outlier: 4.686A pdb=" N LEU C 660 " --> pdb=" O ASN C 656 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 663 " --> pdb=" O ASP C 659 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.274A pdb=" N VAL A 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL A 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N THR A 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N TYR A 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N CYS A 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.624A pdb=" N LYS A 487 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.123A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.766A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 162 Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 274 removed outlier: 6.632A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.006A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 307 Processing sheet with id=AB1, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB2, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.216A pdb=" N VAL B 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL B 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR B 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N TYR B 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N CYS B 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.702A pdb=" N LYS B 487 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 75 through 76 removed outlier: 7.130A pdb=" N CYS B 54 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.740A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 237 " --> pdb=" O PHE B 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 129 through 130 Processing sheet with id=AB7, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AB8, first strand: chain 'B' and resid 158 through 162 Processing sheet with id=AB9, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.700A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.688A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE B 358 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE B 468 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 271 through 273 removed outlier: 3.648A pdb=" N HIS B 330 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG B 419 " --> pdb=" O TYR B 384 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS B 421 " --> pdb=" O PHE B 382 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 304 through 308 Processing sheet with id=AC4, first strand: chain 'C' and resid 35 through 39 Processing sheet with id=AC5, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.818A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 53 through 55 removed outlier: 3.509A pdb=" N PHE C 53 " --> pdb=" O CYS C 218 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.831A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 169 through 177 removed outlier: 4.693A pdb=" N GLU C 190 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.856A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.517A pdb=" N VAL C 286 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU C 452 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AD3, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.555A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG C 419 " --> pdb=" O TYR C 384 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 423 through 424 455 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4660 1.35 - 1.47: 3859 1.47 - 1.60: 6490 1.60 - 1.73: 0 1.73 - 1.85: 144 Bond restraints: 15153 Sorted by residual: bond pdb=" N GLY C 521 " pdb=" CA GLY C 521 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.43e+00 bond pdb=" N GLY B 521 " pdb=" CA GLY B 521 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.92e+00 bond pdb=" N GLY A 521 " pdb=" CA GLY A 521 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.90e+00 bond pdb=" C1 NAG X 1 " pdb=" O5 NAG X 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.52e+00 bond pdb=" C1 NAG Y 1 " pdb=" C2 NAG Y 1 " ideal model delta sigma weight residual 1.532 1.490 0.042 2.00e-02 2.50e+03 4.48e+00 ... (remaining 15148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 20314 2.96 - 5.92: 228 5.92 - 8.88: 24 8.88 - 11.83: 1 11.83 - 14.79: 1 Bond angle restraints: 20568 Sorted by residual: angle pdb=" C SER C 460 " pdb=" N THR C 461 " pdb=" CA THR C 461 " ideal model delta sigma weight residual 121.70 136.49 -14.79 1.80e+00 3.09e-01 6.75e+01 angle pdb=" N ILE C 622 " pdb=" CA ILE C 622 " pdb=" C ILE C 622 " ideal model delta sigma weight residual 111.45 107.95 3.50 9.30e-01 1.16e+00 1.42e+01 angle pdb=" CB GLU B 584 " pdb=" CG GLU B 584 " pdb=" CD GLU B 584 " ideal model delta sigma weight residual 112.60 118.43 -5.83 1.70e+00 3.46e-01 1.18e+01 angle pdb=" CB MET C 475 " pdb=" CG MET C 475 " pdb=" SD MET C 475 " ideal model delta sigma weight residual 112.70 122.97 -10.27 3.00e+00 1.11e-01 1.17e+01 angle pdb=" CA CYS B 418 " pdb=" CB CYS B 418 " pdb=" SG CYS B 418 " ideal model delta sigma weight residual 114.40 122.03 -7.63 2.30e+00 1.89e-01 1.10e+01 ... (remaining 20563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.26: 9745 25.26 - 50.52: 479 50.52 - 75.78: 75 75.78 - 101.04: 52 101.04 - 126.31: 38 Dihedral angle restraints: 10389 sinusoidal: 5424 harmonic: 4965 Sorted by residual: dihedral pdb=" CA ASN A 462 " pdb=" C ASN A 462 " pdb=" N SER A 463 " pdb=" CA SER A 463 " ideal model delta harmonic sigma weight residual 180.00 -145.69 -34.31 0 5.00e+00 4.00e-02 4.71e+01 dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -143.24 57.24 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" CB CYS B 218 " pdb=" SG CYS B 218 " pdb=" SG CYS B 247 " pdb=" CB CYS B 247 " ideal model delta sinusoidal sigma weight residual 93.00 41.18 51.82 1 1.00e+01 1.00e-02 3.67e+01 ... (remaining 10386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.192: 2567 0.192 - 0.383: 13 0.383 - 0.574: 1 0.574 - 0.766: 0 0.766 - 0.957: 1 Chirality restraints: 2582 Sorted by residual: chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN B 448 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.44 -0.96 2.00e-01 2.50e+01 2.29e+01 chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 618 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN B 392 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.73 0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 2579 not shown) Planarity restraints: 2547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 84 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.94e+00 pdb=" C ILE A 84 " -0.046 2.00e-02 2.50e+03 pdb=" O ILE A 84 " 0.017 2.00e-02 2.50e+03 pdb=" N HIS A 85 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 584 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.76e+00 pdb=" CD GLU A 584 " -0.045 2.00e-02 2.50e+03 pdb=" OE1 GLU A 584 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU A 584 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 392 " 0.020 2.00e-02 2.50e+03 1.85e-02 4.29e+00 pdb=" CG ASN B 392 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN B 392 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B 392 " -0.022 2.00e-02 2.50e+03 pdb=" C1 NAG X 1 " 0.020 2.00e-02 2.50e+03 ... (remaining 2544 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 445 2.71 - 3.26: 14377 3.26 - 3.80: 21141 3.80 - 4.35: 26783 4.35 - 4.90: 46139 Nonbonded interactions: 108885 Sorted by model distance: nonbonded pdb=" OE1 GLN A 258 " pdb=" OG1 THR A 387 " model vdw 2.159 3.040 nonbonded pdb=" O3 NAG C 701 " pdb=" O6 NAG C 701 " model vdw 2.186 3.040 nonbonded pdb=" OD1 ASN C 136 " pdb=" ND2 ASN C 156 " model vdw 2.203 3.120 nonbonded pdb=" OE1 GLU B 211 " pdb=" O4 NAG B 705 " model vdw 2.219 3.040 nonbonded pdb=" O ILE A 595 " pdb=" ND2 ASN A 651 " model vdw 2.255 3.120 ... (remaining 108880 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and resid 34 through 708) } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'E' and resid 1) selection = (chain 'F' and resid 1) selection = (chain 'H' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'L' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'b' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'e' and resid 1) selection = (chain 'f' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'h' and resid 1) selection = (chain 'i' and resid 1) selection = (chain 'j' and resid 1) } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.040 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 15269 Z= 0.261 Angle : 0.902 14.792 20883 Z= 0.414 Chirality : 0.056 0.957 2582 Planarity : 0.004 0.058 2502 Dihedral : 17.148 126.305 7074 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.68 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.20), residues: 1689 helix: 0.52 (0.28), residues: 397 sheet: -1.04 (0.25), residues: 411 loop : -1.42 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 504 TYR 0.025 0.002 TYR C 191 PHE 0.010 0.001 PHE A 353 TRP 0.013 0.001 TRP B 631 HIS 0.006 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00558 (15153) covalent geometry : angle 0.83250 (20568) SS BOND : bond 0.00560 ( 33) SS BOND : angle 1.68757 ( 66) hydrogen bonds : bond 0.21327 ( 455) hydrogen bonds : angle 8.15595 ( 1260) link_BETA1-4 : bond 0.00689 ( 38) link_BETA1-4 : angle 3.54400 ( 114) link_NAG-ASN : bond 0.00560 ( 45) link_NAG-ASN : angle 2.86202 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8807 (tpt) cc_final: 0.7773 (tpt) REVERT: A 269 GLU cc_start: 0.7565 (mm-30) cc_final: 0.6635 (tt0) REVERT: A 427 TRP cc_start: 0.6926 (m-10) cc_final: 0.6683 (m-90) REVERT: A 607 ASN cc_start: 0.7349 (t0) cc_final: 0.7080 (t0) REVERT: A 632 ASP cc_start: 0.8177 (t70) cc_final: 0.7794 (t0) REVERT: B 271 MET cc_start: 0.7366 (mmm) cc_final: 0.7141 (tpt) REVERT: B 308 ARG cc_start: 0.8581 (ptp-110) cc_final: 0.8379 (ptp-110) REVERT: B 584 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7377 (mt-10) REVERT: B 614 TRP cc_start: 0.7696 (m-10) cc_final: 0.7392 (m-90) REVERT: C 502 LYS cc_start: 0.7348 (tttm) cc_final: 0.6535 (mttt) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1405 time to fit residues: 36.5780 Evaluate side-chains 151 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.0370 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.143529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.123659 restraints weight = 19100.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.123083 restraints weight = 23665.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.123363 restraints weight = 26114.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.123783 restraints weight = 24596.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.123947 restraints weight = 21847.028| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15269 Z= 0.133 Angle : 0.718 16.032 20883 Z= 0.333 Chirality : 0.048 0.484 2582 Planarity : 0.004 0.039 2502 Dihedral : 12.610 100.657 3834 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.50 % Favored : 95.38 % Rotamer: Outliers : 0.92 % Allowed : 4.92 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.20), residues: 1689 helix: 0.97 (0.29), residues: 402 sheet: -0.78 (0.25), residues: 405 loop : -1.43 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 542 TYR 0.009 0.001 TYR B 484 PHE 0.022 0.002 PHE C 53 TRP 0.013 0.001 TRP B 631 HIS 0.005 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00294 (15153) covalent geometry : angle 0.65719 (20568) SS BOND : bond 0.00402 ( 33) SS BOND : angle 1.19534 ( 66) hydrogen bonds : bond 0.04361 ( 455) hydrogen bonds : angle 5.78780 ( 1260) link_BETA1-4 : bond 0.00561 ( 38) link_BETA1-4 : angle 2.05758 ( 114) link_NAG-ASN : bond 0.00490 ( 45) link_NAG-ASN : angle 3.09537 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 69 TRP cc_start: 0.6604 (p-90) cc_final: 0.5069 (p-90) REVERT: A 161 MET cc_start: 0.8279 (tpt) cc_final: 0.7523 (tpt) REVERT: A 427 TRP cc_start: 0.7604 (m-10) cc_final: 0.7381 (m-90) REVERT: A 542 ARG cc_start: 0.8197 (ttp-110) cc_final: 0.7910 (ttm110) REVERT: A 607 ASN cc_start: 0.7519 (t0) cc_final: 0.7243 (t0) REVERT: B 69 TRP cc_start: 0.6516 (p-90) cc_final: 0.5647 (p-90) REVERT: B 104 MET cc_start: 0.8532 (tpp) cc_final: 0.7883 (ttt) REVERT: B 271 MET cc_start: 0.7692 (mmm) cc_final: 0.7415 (tpt) REVERT: B 308 ARG cc_start: 0.8116 (ptp-110) cc_final: 0.7896 (ptp-110) REVERT: B 387 THR cc_start: 0.8892 (p) cc_final: 0.7920 (m) REVERT: B 647 GLU cc_start: 0.8367 (pt0) cc_final: 0.7817 (pt0) REVERT: C 125 LEU cc_start: 0.9218 (tp) cc_final: 0.8918 (tp) REVERT: C 502 LYS cc_start: 0.7579 (tttm) cc_final: 0.7294 (mttt) REVERT: C 621 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6848 (mt-10) outliers start: 14 outliers final: 8 residues processed: 170 average time/residue: 0.1378 time to fit residues: 34.1549 Evaluate side-chains 148 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain C residue 184 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 5 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 119 optimal weight: 0.0870 chunk 86 optimal weight: 0.4980 chunk 40 optimal weight: 0.0870 chunk 38 optimal weight: 0.0470 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN B 422 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.145763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.125365 restraints weight = 19126.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.125331 restraints weight = 20582.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.125482 restraints weight = 20715.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.125638 restraints weight = 19720.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.125740 restraints weight = 19562.198| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15269 Z= 0.104 Angle : 0.642 11.767 20883 Z= 0.298 Chirality : 0.047 0.510 2582 Planarity : 0.003 0.057 2502 Dihedral : 8.557 57.455 3834 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.97 % Favored : 95.97 % Rotamer: Outliers : 1.44 % Allowed : 7.15 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.21), residues: 1689 helix: 1.20 (0.29), residues: 401 sheet: -0.47 (0.26), residues: 402 loop : -1.35 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 504 TYR 0.007 0.001 TYR A 486 PHE 0.023 0.001 PHE C 53 TRP 0.019 0.001 TRP B 631 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00226 (15153) covalent geometry : angle 0.58884 (20568) SS BOND : bond 0.00427 ( 33) SS BOND : angle 1.30695 ( 66) hydrogen bonds : bond 0.03498 ( 455) hydrogen bonds : angle 5.09295 ( 1260) link_BETA1-4 : bond 0.00480 ( 38) link_BETA1-4 : angle 1.95072 ( 114) link_NAG-ASN : bond 0.00374 ( 45) link_NAG-ASN : angle 2.61380 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 69 TRP cc_start: 0.6440 (p-90) cc_final: 0.5217 (p-90) REVERT: A 100 MET cc_start: 0.8288 (mtm) cc_final: 0.8004 (mtp) REVERT: A 161 MET cc_start: 0.8253 (tpt) cc_final: 0.7550 (tpt) REVERT: A 542 ARG cc_start: 0.8217 (ttp-110) cc_final: 0.7885 (ttm110) REVERT: A 607 ASN cc_start: 0.7829 (t0) cc_final: 0.7479 (t0) REVERT: B 69 TRP cc_start: 0.6609 (p-90) cc_final: 0.5523 (p-90) REVERT: B 104 MET cc_start: 0.8456 (tpp) cc_final: 0.8191 (ttt) REVERT: B 271 MET cc_start: 0.7594 (mmm) cc_final: 0.7342 (tpt) REVERT: B 308 ARG cc_start: 0.8033 (ptp-110) cc_final: 0.7819 (ptp-110) REVERT: B 387 THR cc_start: 0.8702 (p) cc_final: 0.7637 (m) REVERT: B 502 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7357 (tmtt) REVERT: B 647 GLU cc_start: 0.8345 (pt0) cc_final: 0.7858 (pt0) REVERT: C 125 LEU cc_start: 0.9177 (tp) cc_final: 0.8737 (tp) REVERT: C 502 LYS cc_start: 0.7601 (tttm) cc_final: 0.7119 (mtmt) outliers start: 22 outliers final: 12 residues processed: 178 average time/residue: 0.1363 time to fit residues: 35.6340 Evaluate side-chains 154 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 595 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 40 optimal weight: 0.0170 chunk 25 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.142372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.122875 restraints weight = 19222.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.121480 restraints weight = 20344.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.121592 restraints weight = 22252.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.121871 restraints weight = 21663.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.122003 restraints weight = 20602.228| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15269 Z= 0.143 Angle : 0.647 11.160 20883 Z= 0.308 Chirality : 0.047 0.503 2582 Planarity : 0.004 0.056 2502 Dihedral : 7.535 59.583 3834 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.32 % Favored : 95.62 % Rotamer: Outliers : 1.84 % Allowed : 9.12 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.20), residues: 1689 helix: 1.21 (0.29), residues: 401 sheet: -0.54 (0.25), residues: 410 loop : -1.41 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 419 TYR 0.009 0.001 TYR A 484 PHE 0.020 0.002 PHE C 53 TRP 0.013 0.001 TRP B 631 HIS 0.007 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00342 (15153) covalent geometry : angle 0.59414 (20568) SS BOND : bond 0.00452 ( 33) SS BOND : angle 1.53613 ( 66) hydrogen bonds : bond 0.03705 ( 455) hydrogen bonds : angle 4.94933 ( 1260) link_BETA1-4 : bond 0.00408 ( 38) link_BETA1-4 : angle 1.81029 ( 114) link_NAG-ASN : bond 0.00342 ( 45) link_NAG-ASN : angle 2.64808 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.8322 (tpt) cc_final: 0.7521 (ttt) REVERT: A 308 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7300 (tpp-160) REVERT: A 542 ARG cc_start: 0.8320 (ttp-110) cc_final: 0.8058 (ttm110) REVERT: B 69 TRP cc_start: 0.6599 (p-90) cc_final: 0.5792 (p-90) REVERT: B 104 MET cc_start: 0.8467 (tpp) cc_final: 0.8234 (ttt) REVERT: B 180 ASP cc_start: 0.8134 (t0) cc_final: 0.7318 (t0) REVERT: B 271 MET cc_start: 0.7527 (mmm) cc_final: 0.7238 (tpt) REVERT: B 387 THR cc_start: 0.8861 (p) cc_final: 0.8626 (t) REVERT: B 647 GLU cc_start: 0.8384 (pt0) cc_final: 0.7858 (pt0) REVERT: C 502 LYS cc_start: 0.7641 (tttm) cc_final: 0.7386 (mttt) outliers start: 28 outliers final: 14 residues processed: 165 average time/residue: 0.1348 time to fit residues: 32.9063 Evaluate side-chains 152 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 647 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 426 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 100 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 0.0670 chunk 132 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 91 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.143045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.124431 restraints weight = 19065.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.123097 restraints weight = 20714.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.123446 restraints weight = 22676.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.123653 restraints weight = 22514.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.123790 restraints weight = 21180.281| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15269 Z= 0.119 Angle : 0.619 10.319 20883 Z= 0.297 Chirality : 0.046 0.503 2582 Planarity : 0.004 0.056 2502 Dihedral : 7.096 58.290 3834 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.91 % Favored : 95.97 % Rotamer: Outliers : 1.90 % Allowed : 9.65 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.20), residues: 1689 helix: 1.28 (0.29), residues: 399 sheet: -0.59 (0.25), residues: 399 loop : -1.35 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 504 TYR 0.008 0.001 TYR A 191 PHE 0.018 0.002 PHE C 53 TRP 0.012 0.001 TRP B 631 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00276 (15153) covalent geometry : angle 0.56972 (20568) SS BOND : bond 0.00430 ( 33) SS BOND : angle 1.53114 ( 66) hydrogen bonds : bond 0.03407 ( 455) hydrogen bonds : angle 4.79575 ( 1260) link_BETA1-4 : bond 0.00419 ( 38) link_BETA1-4 : angle 1.65036 ( 114) link_NAG-ASN : bond 0.00333 ( 45) link_NAG-ASN : angle 2.52121 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.578 Fit side-chains REVERT: A 161 MET cc_start: 0.8384 (tpt) cc_final: 0.7586 (ttt) REVERT: A 308 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7266 (tpp-160) REVERT: A 542 ARG cc_start: 0.8300 (ttp-110) cc_final: 0.8009 (ttm110) REVERT: B 104 MET cc_start: 0.8504 (tpp) cc_final: 0.8291 (ttt) REVERT: B 180 ASP cc_start: 0.8142 (t0) cc_final: 0.7278 (t0) REVERT: B 271 MET cc_start: 0.7601 (mmm) cc_final: 0.7295 (tpt) REVERT: B 387 THR cc_start: 0.8855 (p) cc_final: 0.8630 (t) REVERT: B 486 TYR cc_start: 0.8557 (m-80) cc_final: 0.8257 (m-10) REVERT: B 530 MET cc_start: 0.6510 (ttp) cc_final: 0.5964 (ttp) REVERT: B 647 GLU cc_start: 0.8381 (pt0) cc_final: 0.7821 (pt0) REVERT: C 125 LEU cc_start: 0.9131 (tp) cc_final: 0.8719 (tp) REVERT: C 161 MET cc_start: 0.7568 (ttm) cc_final: 0.7367 (ttm) REVERT: C 502 LYS cc_start: 0.7673 (tttm) cc_final: 0.7302 (mtmt) REVERT: C 659 ASP cc_start: 0.5433 (m-30) cc_final: 0.5033 (m-30) outliers start: 29 outliers final: 16 residues processed: 166 average time/residue: 0.1303 time to fit residues: 32.2902 Evaluate side-chains 156 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 647 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 426 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 4 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.139765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.119712 restraints weight = 19139.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.119558 restraints weight = 20245.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.119586 restraints weight = 20844.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.119673 restraints weight = 20303.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.119753 restraints weight = 20100.876| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15269 Z= 0.164 Angle : 0.663 10.270 20883 Z= 0.318 Chirality : 0.048 0.516 2582 Planarity : 0.004 0.060 2502 Dihedral : 7.048 59.247 3834 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.80 % Favored : 95.09 % Rotamer: Outliers : 1.64 % Allowed : 11.42 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.20), residues: 1689 helix: 1.23 (0.29), residues: 399 sheet: -0.61 (0.25), residues: 406 loop : -1.40 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 504 TYR 0.011 0.001 TYR A 191 PHE 0.019 0.002 PHE C 53 TRP 0.012 0.001 TRP B 571 HIS 0.008 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00397 (15153) covalent geometry : angle 0.61430 (20568) SS BOND : bond 0.00459 ( 33) SS BOND : angle 1.59973 ( 66) hydrogen bonds : bond 0.03869 ( 455) hydrogen bonds : angle 4.87022 ( 1260) link_BETA1-4 : bond 0.00401 ( 38) link_BETA1-4 : angle 1.64661 ( 114) link_NAG-ASN : bond 0.00359 ( 45) link_NAG-ASN : angle 2.63261 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.524 Fit side-chains REVERT: A 161 MET cc_start: 0.8417 (tpt) cc_final: 0.7627 (ttt) REVERT: A 308 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7487 (tpp-160) REVERT: A 542 ARG cc_start: 0.8271 (ttp-110) cc_final: 0.8021 (ttm110) REVERT: B 104 MET cc_start: 0.8577 (tpp) cc_final: 0.8282 (ttt) REVERT: B 180 ASP cc_start: 0.8219 (t0) cc_final: 0.7340 (t0) REVERT: B 355 ASN cc_start: 0.7114 (p0) cc_final: 0.6515 (t0) REVERT: B 530 MET cc_start: 0.6484 (ttp) cc_final: 0.5998 (ttp) REVERT: B 647 GLU cc_start: 0.8405 (pt0) cc_final: 0.7782 (pt0) REVERT: B 655 LYS cc_start: 0.7641 (tptt) cc_final: 0.7194 (tptt) REVERT: B 658 GLN cc_start: 0.8210 (tt0) cc_final: 0.7867 (tt0) REVERT: C 125 LEU cc_start: 0.9221 (tp) cc_final: 0.8786 (tp) REVERT: C 195 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8280 (p0) REVERT: C 625 ASN cc_start: 0.7543 (t0) cc_final: 0.7135 (t0) REVERT: C 659 ASP cc_start: 0.5466 (m-30) cc_final: 0.5230 (m-30) outliers start: 25 outliers final: 16 residues processed: 156 average time/residue: 0.1315 time to fit residues: 30.3369 Evaluate side-chains 152 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 647 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 426 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 103 optimal weight: 9.9990 chunk 157 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 159 optimal weight: 0.0670 chunk 102 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 119 optimal weight: 0.0870 chunk 43 optimal weight: 0.0870 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.142801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.124805 restraints weight = 18776.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.123679 restraints weight = 21704.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.123775 restraints weight = 22078.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.123928 restraints weight = 21635.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.123999 restraints weight = 20506.818| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15269 Z= 0.110 Angle : 0.624 10.213 20883 Z= 0.299 Chirality : 0.046 0.503 2582 Planarity : 0.003 0.061 2502 Dihedral : 6.816 58.433 3834 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.03 % Favored : 95.86 % Rotamer: Outliers : 1.38 % Allowed : 11.94 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.21), residues: 1689 helix: 1.32 (0.29), residues: 399 sheet: -0.55 (0.26), residues: 371 loop : -1.32 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 504 TYR 0.009 0.001 TYR A 191 PHE 0.017 0.001 PHE C 53 TRP 0.010 0.001 TRP B 571 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00252 (15153) covalent geometry : angle 0.57466 (20568) SS BOND : bond 0.00433 ( 33) SS BOND : angle 1.81359 ( 66) hydrogen bonds : bond 0.03378 ( 455) hydrogen bonds : angle 4.71818 ( 1260) link_BETA1-4 : bond 0.00409 ( 38) link_BETA1-4 : angle 1.57607 ( 114) link_NAG-ASN : bond 0.00348 ( 45) link_NAG-ASN : angle 2.50163 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8386 (tpt) cc_final: 0.7630 (ttt) REVERT: A 308 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7480 (tpp-160) REVERT: A 542 ARG cc_start: 0.8261 (ttp-110) cc_final: 0.8001 (ttm110) REVERT: A 584 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8010 (mt-10) REVERT: B 69 TRP cc_start: 0.6725 (p-90) cc_final: 0.5842 (p-90) REVERT: B 104 MET cc_start: 0.8499 (tpp) cc_final: 0.8237 (ttt) REVERT: B 180 ASP cc_start: 0.8257 (t0) cc_final: 0.7276 (t0) REVERT: B 289 ASN cc_start: 0.8769 (p0) cc_final: 0.8419 (p0) REVERT: B 530 MET cc_start: 0.6451 (ttp) cc_final: 0.5916 (ttp) REVERT: B 647 GLU cc_start: 0.8353 (pt0) cc_final: 0.7761 (pt0) REVERT: C 125 LEU cc_start: 0.9206 (tp) cc_final: 0.8553 (tp) REVERT: C 271 MET cc_start: 0.7997 (mmm) cc_final: 0.7308 (mmt) REVERT: C 625 ASN cc_start: 0.7293 (t0) cc_final: 0.6860 (t0) REVERT: C 659 ASP cc_start: 0.5188 (m-30) cc_final: 0.4980 (m-30) outliers start: 21 outliers final: 13 residues processed: 158 average time/residue: 0.1283 time to fit residues: 30.4464 Evaluate side-chains 154 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 647 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 426 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 93 optimal weight: 0.5980 chunk 96 optimal weight: 0.0170 chunk 170 optimal weight: 0.0570 chunk 131 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 74 optimal weight: 0.1980 chunk 44 optimal weight: 0.6980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.144531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.126933 restraints weight = 18937.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.126660 restraints weight = 23378.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.126822 restraints weight = 22435.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.126957 restraints weight = 21570.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.127026 restraints weight = 19801.983| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15269 Z= 0.101 Angle : 0.599 10.075 20883 Z= 0.287 Chirality : 0.046 0.484 2582 Planarity : 0.003 0.059 2502 Dihedral : 6.496 58.439 3834 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.26 % Favored : 95.68 % Rotamer: Outliers : 1.12 % Allowed : 12.73 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.21), residues: 1689 helix: 1.41 (0.29), residues: 399 sheet: -0.40 (0.27), residues: 371 loop : -1.27 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 504 TYR 0.008 0.001 TYR A 191 PHE 0.016 0.001 PHE C 53 TRP 0.017 0.001 TRP C 35 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00226 (15153) covalent geometry : angle 0.55439 (20568) SS BOND : bond 0.00557 ( 33) SS BOND : angle 1.63408 ( 66) hydrogen bonds : bond 0.03041 ( 455) hydrogen bonds : angle 4.54072 ( 1260) link_BETA1-4 : bond 0.00385 ( 38) link_BETA1-4 : angle 1.52464 ( 114) link_NAG-ASN : bond 0.00330 ( 45) link_NAG-ASN : angle 2.32658 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.8309 (tpt) cc_final: 0.7505 (ttt) REVERT: A 308 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7495 (tpp-160) REVERT: A 540 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7881 (mp10) REVERT: A 584 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8055 (mt-10) REVERT: B 69 TRP cc_start: 0.6650 (p-90) cc_final: 0.5896 (p-90) REVERT: B 180 ASP cc_start: 0.8259 (t0) cc_final: 0.7322 (t0) REVERT: B 289 ASN cc_start: 0.8726 (p0) cc_final: 0.8365 (p0) REVERT: B 486 TYR cc_start: 0.8553 (m-80) cc_final: 0.8166 (m-10) REVERT: B 530 MET cc_start: 0.6373 (ttp) cc_final: 0.5800 (ttp) REVERT: B 647 GLU cc_start: 0.8300 (pt0) cc_final: 0.7920 (pt0) REVERT: C 125 LEU cc_start: 0.8925 (tp) cc_final: 0.8446 (tp) REVERT: C 625 ASN cc_start: 0.7215 (t0) cc_final: 0.6850 (t0) outliers start: 17 outliers final: 11 residues processed: 164 average time/residue: 0.1182 time to fit residues: 29.8233 Evaluate side-chains 155 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 540 GLN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 426 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 107 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 76 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 637 ASN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.143869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.120295 restraints weight = 19260.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.120505 restraints weight = 19459.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.121268 restraints weight = 18610.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.121511 restraints weight = 17217.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.121770 restraints weight = 15781.296| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15269 Z= 0.185 Angle : 0.699 10.198 20883 Z= 0.337 Chirality : 0.048 0.508 2582 Planarity : 0.004 0.058 2502 Dihedral : 6.824 59.530 3834 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.62 % Favored : 94.32 % Rotamer: Outliers : 1.31 % Allowed : 13.19 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.20), residues: 1689 helix: 1.21 (0.29), residues: 399 sheet: -0.64 (0.26), residues: 376 loop : -1.37 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 504 TYR 0.011 0.001 TYR A 486 PHE 0.017 0.002 PHE C 53 TRP 0.016 0.002 TRP C 35 HIS 0.008 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00450 (15153) covalent geometry : angle 0.65006 (20568) SS BOND : bond 0.00523 ( 33) SS BOND : angle 1.86092 ( 66) hydrogen bonds : bond 0.04026 ( 455) hydrogen bonds : angle 4.81326 ( 1260) link_BETA1-4 : bond 0.00411 ( 38) link_BETA1-4 : angle 1.61573 ( 114) link_NAG-ASN : bond 0.00374 ( 45) link_NAG-ASN : angle 2.69886 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.8482 (tpt) cc_final: 0.7729 (ttt) REVERT: A 308 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7570 (tpp-160) REVERT: B 69 TRP cc_start: 0.6731 (p-90) cc_final: 0.5710 (p-90) REVERT: B 180 ASP cc_start: 0.8393 (t0) cc_final: 0.7456 (t0) REVERT: B 207 LYS cc_start: 0.8421 (mmtt) cc_final: 0.8190 (mmtt) REVERT: B 289 ASN cc_start: 0.8824 (p0) cc_final: 0.8461 (p0) REVERT: B 530 MET cc_start: 0.6581 (ttp) cc_final: 0.6125 (ttp) REVERT: B 647 GLU cc_start: 0.8131 (pt0) cc_final: 0.7776 (pt0) REVERT: B 655 LYS cc_start: 0.7452 (tptt) cc_final: 0.7061 (tptt) REVERT: B 658 GLN cc_start: 0.8267 (tt0) cc_final: 0.8003 (tt0) REVERT: B 664 ASP cc_start: 0.7414 (p0) cc_final: 0.7163 (p0) REVERT: C 625 ASN cc_start: 0.7456 (t0) cc_final: 0.7082 (t0) outliers start: 20 outliers final: 15 residues processed: 154 average time/residue: 0.1348 time to fit residues: 30.7191 Evaluate side-chains 153 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 426 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 168 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 1 optimal weight: 0.2980 chunk 127 optimal weight: 0.5980 chunk 99 optimal weight: 0.1980 chunk 116 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 148 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.147955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.125187 restraints weight = 18989.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.125328 restraints weight = 18947.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.126121 restraints weight = 19359.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.126351 restraints weight = 17403.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.127475 restraints weight = 15797.819| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15269 Z= 0.112 Angle : 0.625 10.104 20883 Z= 0.299 Chirality : 0.046 0.495 2582 Planarity : 0.003 0.059 2502 Dihedral : 6.533 58.193 3834 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.09 % Favored : 95.86 % Rotamer: Outliers : 1.05 % Allowed : 13.85 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.21), residues: 1689 helix: 1.35 (0.29), residues: 399 sheet: -0.48 (0.25), residues: 407 loop : -1.33 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 504 TYR 0.014 0.001 TYR C 486 PHE 0.016 0.001 PHE C 53 TRP 0.012 0.001 TRP C 35 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00257 (15153) covalent geometry : angle 0.58154 (20568) SS BOND : bond 0.00461 ( 33) SS BOND : angle 1.34331 ( 66) hydrogen bonds : bond 0.03273 ( 455) hydrogen bonds : angle 4.59150 ( 1260) link_BETA1-4 : bond 0.00387 ( 38) link_BETA1-4 : angle 1.51259 ( 114) link_NAG-ASN : bond 0.00321 ( 45) link_NAG-ASN : angle 2.47213 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8403 (tpt) cc_final: 0.7617 (ttt) REVERT: A 308 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7554 (tpp-160) REVERT: B 69 TRP cc_start: 0.6637 (p-90) cc_final: 0.5712 (p-90) REVERT: B 180 ASP cc_start: 0.8360 (t0) cc_final: 0.7439 (t0) REVERT: B 289 ASN cc_start: 0.8777 (p0) cc_final: 0.8416 (p0) REVERT: B 530 MET cc_start: 0.6510 (ttp) cc_final: 0.5981 (ttp) REVERT: B 655 LYS cc_start: 0.7401 (tptt) cc_final: 0.6944 (tttt) REVERT: C 625 ASN cc_start: 0.7349 (t0) cc_final: 0.7044 (t0) outliers start: 16 outliers final: 14 residues processed: 157 average time/residue: 0.1301 time to fit residues: 30.3015 Evaluate side-chains 155 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 426 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 83 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 152 optimal weight: 0.4980 chunk 119 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 105 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.146788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.123841 restraints weight = 18887.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.125161 restraints weight = 16499.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.125257 restraints weight = 14263.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.125470 restraints weight = 14086.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.125606 restraints weight = 13572.770| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15269 Z= 0.114 Angle : 0.632 10.050 20883 Z= 0.300 Chirality : 0.046 0.484 2582 Planarity : 0.003 0.055 2502 Dihedral : 6.407 58.914 3834 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.38 % Favored : 95.56 % Rotamer: Outliers : 1.38 % Allowed : 13.45 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.21), residues: 1689 helix: 1.37 (0.29), residues: 399 sheet: -0.45 (0.26), residues: 411 loop : -1.32 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 504 TYR 0.014 0.001 TYR C 486 PHE 0.016 0.001 PHE C 53 TRP 0.011 0.001 TRP B 631 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00264 (15153) covalent geometry : angle 0.58529 (20568) SS BOND : bond 0.00437 ( 33) SS BOND : angle 1.31162 ( 66) hydrogen bonds : bond 0.03232 ( 455) hydrogen bonds : angle 4.54331 ( 1260) link_BETA1-4 : bond 0.00399 ( 38) link_BETA1-4 : angle 1.52554 ( 114) link_NAG-ASN : bond 0.00316 ( 45) link_NAG-ASN : angle 2.60603 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2121.99 seconds wall clock time: 37 minutes 43.97 seconds (2263.97 seconds total)